Re: ABySS issues (user error)

[Shaun Jackman]

Hi Erika,

Please direct your ABySS-related questions to the ABySS mailing list, cc’ed on this email.
http://groups.google.com/group/abyss-users
abyss...@googlegroups.com

The version of ABySS that you’re using appears rather old. I’d suggest upgrading to ABySS 1.3.3, which you can download here:
http://www.bcgsc.ca/platform/bioinfo/software/abyss

ABySS 1.3.3 should be able to assemble your data without needing to add /1 and /2 to the reads.

Cheers,
Shaun

On 2012-05-20, at 7:52 , Erika N.Schwarz wrote:

> Hi Shaun,
>
> I'm sorry to email you directly about this but I keep getting an error message in ABySS when trying to assemble my 100bp paired end Illumina data. Nobody else in my lab has used ABySS and I have been Googling for days and going through all of the ABySS threads but I can't find what I'm looking for. I am new to Illumina, genome assembly and Unix (the perfect storm) so most things are going over my head I think. I have two files, Tr_R1.fastq and Tr_R2.fastq, that I have been putting into the abyss command line (abyss-pe k=50 n=20 in='Tr_R1.fastq Tr_R2.fastq' name=T_repens) to run. I got the error message below and then I found a Perl script on one of the boards that should have put a 1 or 2 on the ends of all of my reads. I ran that, erased any files the the first run generated and then ran ABySS again with my new files, Tr_fix_R1.fastq and Tr_fix_R2.fastq. I still got this error message. What am I doing wrong?
>
> PopBubbles -j2 -k50 -p0.9 -g T_repens-3.adj T_repens-1.fa T_repens-1.adj >T_r$
> MergeContigs -k50 -o T_repens-3.fa T_repens-1.fa T_repens-1.adj T_repens-1.path
> The minimum coverage of single-end contigs is 2.
> The minimum coverage of merged contigs is 2.
> awk '!/^>/ {x[">" $1]=1; next} {getline s} $1 in x {print $0 "\n" s}' \
> T_repens-1.path T_repens-1.fa >T_repens-indel.fa
> KAligner -i -j2 -k50 Tr_fix_R1.fastq Tr_fix_R2.fastq T_repens-3.fa \
> |ParseAligns -k50 -h T_repens-3.hist \
> |sort -snk3 -k4 \
> |gzip >T_repens-3.sam.gz
> Found 4118 (0.000898074%) duplicate k-mer.
> error: read ID `HWI-ST1097:96:D0UD7ACXX:1:1101:1436:2098' must end in one of
> 1 and 2 or A and B or F and R or F3 and R3 or forward and reverse
> gunzip -c T_repens-3.sam.gz \
> |DistanceEst -j2 -k50 -s100 -n20 -o T_repens-3.dist T_repens-3.hist
> T_repens-3.hist: No such file or directory
> make: *** [T_repens-3.dist] Error 1
> make: *** Deleting file `T_repens-3.dist'
>
> Thank you for any help,
> Erika
>
> _________________________________
> Erika N. Schwarz
>
> Plant Biology Graduate Program
> University of Texas at Austin
> ensc...@utexas.edu
>
> "No man should escape our universities without knowing how little he knows." ~ Charles Darwin